Model compounds, such as 12-Aminohexadecanoic acid and kaolinite, mare utilized to simulate adsorption under different salinities. The experiments showed that the total organic carbon content adsorbed to kaolinite is 0.166% and 0.082% under high and low salinity conditions, respectively. The kaolinite (001) adsorption behavior of organic matter was simulated by molecular dynamics (MD) technology in the presence of Na+. In addition, the adsorption process was not only statistically analysed but the adsorption energy of state organic matter at the clay surface and the sources of adsorption energy are calculated. It is shown that the increase of Na+ is conducive to the adsorption of the organic matter, which is also supported by the experimental results. The adsorption of organic matter is mainly controlled by functional groups of -CH2 on the kaolinite surface. Density functional theory (DFT) calculations further indicate that the 2 s orbital of Na+ is hybridized with -OH of kaolinite and the 2p orbital of -COO- of 12-Aminohexadecanoic acid under bridging action. Thus, the electron compensation mechanism of Na+ was clarified. This study provides a molecular perspective on the interaction mechanisms between organic matter and kaolinite, which is beneficial to the field of biogeochemistry and environmental effects.